A core calculus for the analysis and implementation of biologically inspired languages

The application of Concurrency Theory to Systems Biology is in its earliest stage of progress. The metaphor of cells as computing systems by Regev and Shapiro opened the employment of concurrent languages for the modelling of biological systems. Their peculiar characteristics led to the design of many bio-inspired formalisms which achieve higher faithfulness and specificity. In this thesis we present pi@, an extremely simple and conservative extension of the pi-calculus representing a keystone in this respect, thanks to its expressiveness capabilities. The pi@ calculus is obtained by the addition of polyadic synchronisation and priority to the pi-calculus, in order to achieve compartment semantics and atomicity of complex operations respectively. In its direct application to biological modelling, the stochastic variant of the calculus, Spi@, is shown able to model consistently several phenomena such as formation of molecular complexes, hierarchical subdivision of the system into compartments, inter-compartment reactions, dynamic reorganisation of compartment structure consistent with volume variation. The pivotal role of pi@ is evidenced by its capability of encoding in a compositional way several bio-inspired formalisms, so that it represents the optimal core of a framework for the analysis and implementation of bio-inspired languages. In this respect, the encodings of BioAmbients, Brane Calculi and a variant of P Systems in pi@ are formalised. The conciseness of their translation in pi@ allows their indirect comparison by means of their encodings. Furthermore it provides a ready-to-run implementation of minimal effort whose correctness is granted by the correctness of the respective encoding functions. Further important results of general validity are stated on the expressive power of priority. Several impossibility results are described, which clearly state the superior expressiveness of prioritised languages and the problems arising in the attempt of providing their parallel implementation. To this aim, a new setting in distributed computing (the last man standing problem) is singled out and exploited to prove the impossibility of providing a purely parallel implementation of priority by means of point-to-point or broadcast communication.

Studio longitudinale della funzione cardiaca materna nelle gravidanze gemellari

Obiettivo: studio longitudinale di una coorte di gravidanze gemellari e valutazione di eventuali correlazioni tra specifici parametri cardiaci materni ed esito sfavorevole della gravidanza. Metodi: Sono state arruolate in modo prospettico donne con gravidanze gemellari, sottoposte a controlli seriati della funzione cardiaca materna ( 20-23 settimane; 26-29 settimane e 30-33 settimane). Le pazienti in cui il parto si è verificato prima della 34°settimana compiuta di gestazione sono state escluse a priori dallo studio. Specifici parametri cardiaci campionati sono stati confrontati tra il gruppo di gravidanze con esito positivo ed il gruppo di pazienti che hanno sviluppato complicanze nel corso della gravidanza quali: preeclampsia o ipertensione gestazionale, basso peso alla nascita ( SGA: peso neonatale di uno o entrambi i feti < 5° centile per l’epoca di gestazione). Risultati: sono state incluse nello studio 28 gravidanze gemellari,di cui 8 complicate. Durante ogni visita abbiamo osservato un aumento significativo della gittata cardiaca ( CO ) e sistolica ( SV ) ed una caduta delle resistenze vascolari totali ( TVR ) nelle gravidanze gemellari normali vs complicate. Inoltre, CO, pressione arteriosa (BP), frequenza cardiaca ( HR ) e TVR son rimaste invariate nel corso dei controlli ambulatoriali per le gravidanze con esiti sfavorevole, mentre mostravano modificazioni significative ( CO, HR e BDP in aumento; TVR in diminuzione ) nel gruppo di pazienti con esito favorevole della gravidanza. Conclusioni: La valutazione longitudinale della funzione cardiaca materna sembra dimostrare una significativa differenza tra i valori dei parametri cardiaci materni delle gravidanze multiple non complicate, rispetto a quelle complicate da preeclampsia o neonati SGA.

Strategia terapeutica nei pazienti con ipertensione arteriosa polmonare a rischio intermedio

Le attuali linee guida stratificano il rischio dei pazienti con ipertensione arteriosa polmonare (IAP) in basso, intermedio e alto (rispettivamente con mortalità a 1 anno <5%, 5-10% e >10%). La maggior parte dei pazienti è però classificata nella categoria intermedia. Per stratificare ulteriormente questi pazienti, abbiamo valutato il ruolo prognostico dello stroke volume index (SVI) misurato al cateterismo cardiaco destro (CCDx) in 725 pazienti naïve da terapia con IAP idiopatica/ereditaria, associata a malattie del tessuto connettivo o cardiopatie congenite. I pazienti sono stati valutati al basale e 3-4 mesi dopo l'inizio della terapia (1° F-UP) con CCDx, livelli plasmatici di peptide natriuretico cerebrale (BNP), test dei 6 minuti (T6M) e classe funzionale OMS. Abbiamo applicato una tabella di rischio semplificata utilizzando i criteri: classe funzionale OMS, T6M, pressione atriale destra o livelli plasmatici di BNP e indice cardiaco (IC) o saturazione di ossigeno venoso misto (SvO2). Le classi di rischio sono state definite come: basso= almeno 3 criteri a basso rischio e nessun criterio ad alto rischio; alto= almeno 2 criteri ad alto rischio inclusi IC o SvO2; intermedio= tutti gli altri casi. Lo SVI, mediante la regressione di Cox, stratifica la prognosi dei pazienti a rischio intermedio al 1° F-UP [p=0.008] ma non al basale [p=0.085]. Considerandone l’ottimale cut-off predittivo (38 ml/m2) i pazienti a rischio intermedio sono ulteriormente classificabili in intermedio-basso e intermedio-alto. Considerando l'effetto dei 3 principali farmaci che agiscono sulla via della prostaciclina in aggiunta alla duplice terapia di combinazione con inibitori della fosfodiesterasi-5 e antagonisti dell'endotelina, i pazienti trattati con epoprostenolo e.v. hanno ottenuto un maggiore miglioramento rispetto ai pazienti trattati con selexipag; col treprostinil s.c. vi è stata una risposta intermedia. Abbiamo quindi proposto un algoritmo di terapia con selexipag in pazienti a rischio intermedio-basso e con prostanoidi parenterali in pazienti a rischio intermedio-alto.

Alterazioni strutturali e funzionali nelle diverse eziologie di amiloidosi cardiaca: analisi dei parametri ecocardiografici ed emodinamici invasivi e loro ruolo prognostico

Background e scopo: Tradizionalmente la cardiomiopatia amiloidotica (CA) è stata considerata una cardiomiopatia restrittiva, ma studi recenti hanno evidenziato il ruolo anche della disfuzione sistolica nella sua fisiopatologia. In questo contesto recente, raramente è stato indagato il profilo emodinamico invasivo. Lo scopo dello studio è stato quello di caratterizzare il profilo emodinamico, strutturale e funzionale della CA nelle tre principali eziologie (amiloidosi da catene leggere (AL), amiloidosi transtiretino-relata (ATTR) mutata (ATTRm) e ‘wild-type’ (ATTRwt)), valutare le differenze del profilo ecocardiografico ed emodinamico nelle fasi diverse di malattia ed esplorare il ruolo prognostico delle principali variabili cliniche e strumentali nella CA. Metodi e risultati: Abbiamo analizzato retrospettivamente i dati di 224 pazienti con CA (AL, n=93; ATTRm, n=66; ATTRwt, n=65). Rispetto all'ATTRwt, i pazienti con AL presentano un minor interessamento morfologico cardiaco, ma dati emodinamici paragonabili, caratterizzati da elevate pressioni di riempimento biventricolari e riduzione della gittata sistolica. L’ATTRm, nonostante il profilo ecocardiografico analogo all’ATTRwt, mostra un quadro emodinamico migliore. Gli indici di funzione diastolica e sistolica longitudinale del ventricolo sinistro (Vsn) sono alterati fin dagli stadi iniziali della malattia, mentre la frazione di eiezione (FEVsn) rimane preservata nella maggior parte dei pazienti, anche nelle fasi avanzate (FEVsn 50 [37-60]%; FEVsn <40% nel 28% dei pazienti NYHA III / IV). All'analisi multivariata, età, NYHA III/I, eziologia AL, frazione di contrazione miocardica (MCF), indice cardiaco (CI) e pressione atriale destra (RAP) sono indipendentemente associati a eventi clinici avversi. Conclusioni Questo studio conferma la complessa fisiopatologia della CA, in cui la disfunzione diastolica è accompagnata da una funzione sistolica longitudinale anormale sin dalle fasi iniziali della malattia. L'AL e l'ATTRwt, nonostante diversi gradi di alterazioni morfologiche, hanno un profilo emodinamico simile; l'ATTRm, invece, presenta un quadro emodinamico migliore. Tra i parametri strumentali, MCF, CI e RAP emergono come predittori significativi di eventi avversi.

Genotypic variation in Actinidia deliciosa fruit size and carbohydrate content

In a global and increasingly competitive fresh produce market, more attention is being given to fruit quality traits and consumer satisfaction. Kiwifruit occupies a niche position in the worldwide market, when compared to apples, oranges or bananas. It is a fruit with extraordinarily good nutritional traits, and its benefits to human health have been widely described. Until recently, international trade in kiwifruit was restricted to a single cultivar, but different types of kiwifruit are now becoming available in the market. Effective programmes of kiwifruit improvement start by considering the requirements of consumers, and recent surveys indicate that sweeter fruit with better flavour are generally preferred. There is a strong correlation between at-harvest dry matter and starch content, and soluble solid concentration and flavour when fruit are eating ripe. This suggests that carbon accumulation strongly influences the development of kiwifruit taste. The overall aim of the present study was to determine what factors affect carbon accumulation during Actinidia deliciosa berry development. One way of doing this is by comparing kiwifruit genotypes that differ greatly in their ability to accumulate dry matter in their fruit. Starch is the major component of dry matter content. It was hypothesized that genotypes were different in sink strength. Sink strength, by definition, is the effect of sink size and sink activity. Chapter 1 reviews fruit growth, kiwifruit growth and development and carbon metabolism. Chapter 2 describes the materials and methods used. Chapter 3, 4, 5 and 6 describes different types of experimental work. Chapter 7 contains the final discussions and the conclusions Three Actinidia deliciosa breeding populations were analysed in detail to confirm that observed differences in dry matter content were genetically determined. Fruit of the different genotypes differed in dry matter content mainly because of differences in starch concentrations and dry weight accumulation rates, irrespective of fruit size. More detailed experiments were therefore carried out on genotypes which varied most in fruit starch concentrations to determine why sink strengths were so different. The kiwifruit berry comprises three tissues which differ in dry matter content. It was initially hypothesised that observed differences in starch content could be due to a larger proportion of one or other of these tissues, for example, of the central core which is highest in dry matter content. The study results showed that this was not the case. Sink size, intended as cell number or cell size, was then investigated. The outer pericarp makes up about 60% of berry weight in ‘Hayward’ kiwifruit. The outer pericarp contains two types of parenchyma cells: large cells with low starch concentration, and small cells with high starch concentration. Large cell, small cell and total cell densities in the outer pericarp were shown to be not correlated with either dry matter content or fruit size but further investigation of volume proportion among cell types seemed justified. It was then shown that genotypes with fruit having higher dry matter contents also had a higher proportion of small cells. However, the higher proportion of small cell volume could only explain half of the observed differences in starch content. So, sink activity, intended as sucrose to starch metabolism, was investigated. In transiently starch storing sinks, such as tomato fruit and potato tubers, a pivotal role in carbon metabolism has been attributed to sucrose cleaving enzymes (mainly sucrose synthase and cell wall invertase) and to ADP-glucose pyrophosphorylase (the committed step in starch synthesis). Studies on tomato and potato genotypes differing in starch content or in final fruit soluble solid concentrations have demonstrated a strong link with either sucrose synthase or ADP-glucose pyrophosphorylase, at both enzyme activity and gene expression levels, depending on the case. Little is known about sucrose cleaving enzyme and ADP-glucose pyrophosphorylase isoforms. The HortResearch Actinidia EST database was then screened to identify sequences putatively encoding for sucrose synthase, invertase and ADP-glucose pyrophosphorylase isoforms and specific primers were designed. Sucrose synthase, invertase and ADP-glucose pyrophosphorylase isoform transcript levels were anlayzed throughout fruit development of a selection of four genotypes (two high dry matter and two low dry matter). High dry matter genotypes showed higher amounts of sucrose synthase transcripts (SUS1, SUS2 or both) and higher ADP-glucose pyrophosphorylase (AGPL4, large subunit 4) gene expression, mainly early in fruit development. SUS1- like gene expression has been linked with starch biosynthesis in several crop (tomato, potato and maize). An enhancement of its transcript level early in fruit development of high dry matter genotypes means that more activated glucose (UDP-glucose) is available for starch synthesis. This can be then correlated to the higher starch observed since soon after the onset of net starch accumulation. The higher expression level of AGPL4 observed in high dry matter genotypes suggests an involvement of this subunit in drive carbon flux into starch. Changes in both enzymes (SUSY and AGPse) are then responsible of higher starch concentrations. Low dry matter genotypes showed generally higher vacuolar invertase gene expression (and also enzyme activity), early in fruit development. This alternative cleavage strategy can possibly contribute to energy loss, in that invertases’ products are not adenylated, and further reactions and transport are needed to convert carbon into starch. Although these elements match well with observed differences in starch contents, other factors could be involved in carbon metabolism control. From the microarray experiment, in fact, several kinases and transcription factors have been found to be differentially expressed. Sink strength is known to be modified by application of regulators. In ‘Hayward’ kiwifruit, the synthetic cytokinin CPPU (N-(2-Chloro-4-Pyridyl)-N-Phenylurea) promotes a dramatic increase in fruit size, whereas dry matter content decreases. The behaviour of CPPU-treated ‘Hayward’ kiwifruit was similar to that of fruit from low dry matter genotypes: dry matter and starch concentrations were lower. However, the CPPU effect was strongly source limited, whereas in genotype variation it was not. Moreover, CPPU-treated fruit gene expression (at sucrose cleavage and AGPase levels) was similar to that in high dry matter genotypes. It was therefore concluded that CPPU promotes both sink size and sink activity, but at different “speeds” and this ends in the observed decrease in dry matter content and starch concentration. The lower “speed” in sink activity is probably due to a differential partitioning of activated glucose between starch storage and cell wall synthesis to sustain cell expansion. Starch is the main carbohydrate accumulated in growing Actinidia deliciosa fruit. Results obtained in the present study suggest that sucrose synthase and AGPase enzymes contribute to sucrose to starch conversion, and differences in their gene expression levels, mainly early in fruit development, strongly affect the rate at which starch is therefore accumulated. This results are interesting in that starch and Actinidia deliciosa fruit quality are tightly connected.

Development of a patient-specific model for stroke risk assessment in atrial fibrillation patients

Atrial fibrillation is associated with a five-fold increase in the risk of cerebrovascular events,being responsible of 15-18% of all strokes.The morphological and functional remodelling of the left atrium caused by atrial fibrillation favours blood stasis and, consequently, stroke risk. In this context, several clinical studies suggest that stroke risk stratification could be improved by using haemodynamic information on the left atrium (LA) and the left atrial appendage (LAA). The goal of this study was to develop a personalized computational fluid-dynamics (CFD) model of the left atrium which could clarify the haemodynamic implications of atrial fibrillation on a patient specific basis. The developed CFD model was first applied to better understand the role of LAA in stroke risk. Infact, the interplay of the LAA geometric parameters such as LAA length, tortuosity, surface area and volume with the fluid-dynamics parameters and the effects of the LAA closure have not been investigated. Results demonstrated the capabilities of the CFD model to reproduce the real physiological behaviour of the blood flow dynamics inside the LA and the LAA. Finally, we determined that the fluid-dynamics parameters enhanced in this research project could be used as new quantitative indexes to describe the different types of AF and open new scenarios for the patient-specific stroke risk stratification.